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The Ultimate Guide to Through Deck Pontoon Trolling Motors on Pontoon Boats

Through Deck Pontoon Trolling Motors on Pontoon Boats

Welcome to the ultimate guide to through deck pontoon trolling motors on pontoon boats. If you’re new to trolling motors, you may be wondering what they are and how they work. Trolling motors are electric-powered motors designed to help control the movement of a boat, primarily for fishing and trolling. In this guide, we’ll cover everything you need to know about through deck trolling motors, including the benefits of this setup and how to select the right trolling motor for your pontoon boat. We’ll also provide installation tips, techniques for optimizing your trolling motor’s performance, and troubleshooting and maintenance advice. By the end of this guide, you’ll be a trolling motor expert, and your fishing trips will be a breeze!

Key takeaway
Selecting the right through deck trolling motor requires consideration of motor type, thrust power, and battery efficiency.

Selecting the Right Through Deck Trolling Motor

When it comes to selecting the right through deck trolling motor for your pontoon boat, there are several factors you need to consider to ensure you make an informed decision. Below, we outline the different types of trolling motors, key features to look for, thrust power requirements, and battery power and efficiency.

Different Types of Trolling Motors Explained

There are three main types of trolling motors available for pontoon boats: bow mount, transom mount, and engine mount. Bow mount trolling motors are mounted at the front of a boat, while transom mount motors are at the rear. Engine mount trolling motors are attached to the boat’s primary engine. Each type has its advantages and disadvantages, so it’s essential to understand which type is best suited for your needs.

Key Features to Look for in a Through Deck Trolling Motor

There are several essential factors to consider when selecting a through deck trolling motor. These include the motor’s thrust power, shaft length, voltage, control type, and weight. The thrust power must match your boat’s weight and desired speed, while the shaft length must be appropriate for your boat’s transom height.

Thrust Power Requirements for Pontoon Boats

Thrust power is a crucial factor in selecting a through deck trolling motor. It determines the speed and maneuverability of the boat, so it’s crucial to get it right. As a general rule, you should select a trolling motor with a minimum thrust power of 55 pounds for a 20 ft pontoon boat. For larger boats, you’ll need more thrust power to achieve the desired speed.

Considering Battery Power and Efficiency

The battery power and efficiency of your through deck trolling motor are crucial for providing enough power to operate the motor effectively. You’ll need to consider the weight of the battery and the battery type carefully. Lithium-ion batteries are an excellent choice for their long-lasting charge and low weight. Additionally, consider investing in a battery charger to keep your battery charged and maximize its efficiency.

In summary, selecting the right through deck trolling motor for your pontoon boat requires careful consideration of several factors, including motor type, thrust power, shaft length, control type, voltage, weight, and battery power and efficiency. Take your boat’s size and weight into account, and ensure you select a motor powerful enough to achieve the desired speed. Remember, a high-quality trolling motor can significantly enhance your boating experience, so it’s worth investing in the right one.

Installation Tips for Through Deck Trolling Motors

Essential Tools and Materials for Installation

Before installing your through deck pontoon trolling motor, you’ll need to ensure you have all the necessary tools and materials. Here’s a quick checklist of everything you’ll need:

  • Electric drill with screwdriver bits and drill bits
  • Wrenches and pliers for tightening bolts and cables
  • Wire cutters and strippers for electrical connections
  • Sealant tape and marine-grade silicone for sealing connections and preventing leaks
  • Through deck trolling motor kit including mounting hardware and cables
  • Battery and battery box with battery cables

Step-by-Step Installation Process

Getting your through deck trolling motor installed on your pontoon boat takes some careful planning and attention to detail. Here’s how to do it:

  1. Choose the right location on your pontoon boat: The location for your trolling motor should be close to the bow and should be free from obstructions. The location should also allow for easy access to the battery compartment.
  2. Prepare the mounting bracket: Attach the mounting bracket to the trolling motor and then attach the bracket to the through deck mount. Don’t tighten the bolts down too much, as you’ll need to make adjustments once the motor is in place.
  3. Create an opening in the deck: Use a hole saw or jigsaw to create an opening in the deck where the motor will be inserted. Be sure to measure carefully and double-check the placement before cutting.
  4. Insert the trolling motor: Slide the trolling motor into the opening in the deck and attach the bracket to the through deck mount. Make any necessary adjustments to the motor location or bracket as needed.
  5. Install the battery: Install the battery and battery box in a secure location near the motor. Connect the battery cables to the motor, ensuring proper polarity.
  6. Wire the trolling motor: Wire the trolling motor per the manufacturer’s instructions, handling cables with care and making sure to seal all connections with silicone and sealant tape to prevent water intrusion.
  7. Test the motor: Test the motor to ensure it is working properly and making sure the propeller is turning in the correct direction before taking your boat out on the water. Adjust the motor if necessary.

Common Installation Challenges and Solutions

Installing a through deck trolling motor can be a tricky process, but some common challenges and solutions can help make the process go more smoothly:

  • Motor location: Choosing the right location for the motor can be challenging, especially if your pontoon boat is already crowded with equipment. Consider installing additional mounts or brackets to accommodate the motor.
  • Cable routing: Running cables and wiring to the motor can be a challenge, especially if you have to route cables around obstructions or existing equipment. Take your time and be sure to route cables in a way that won’t interfere with other systems or equipment.
  • Leak prevention: One of the biggest challenges with through deck trolling motor installation is preventing leaks. Be sure to use plenty of silicone and sealant tape to cover all connections and create a water-tight seal.

Maintenance and Care Post-Installation

Once your through deck trolling motor is installed and working properly, it’s important to keep up with routine maintenance and care to ensure it stays in good working order:

  • Inspect connections: Regularly inspect all wiring and connections to ensure they are tight and secure. Replace any damaged wiring or connectors immediately.
  • Clean the motor: Clean the motor regularly to prevent buildup of debris or grime that could interfere with performance. Use a mild detergent and water to clean the motor, taking care not to get water inside any electrical components.
  • Check propeller: Check the propeller for damage or wear and tear, replacing it if necessary. Keep the propeller free from debris and submerged weeds to prevent damage.

Techniques for Optimizing Trolling Motor Performance

Using a trolling motor on a pontoon boat requires some technique to optimize its performance, conserve battery life, and handle different water conditions effortlessly. Below are some best practices and tips to help you make the most out of your trolling motor.

Best Practices for Maneuvering with a Trolling Motor

  • Use the lowest possible speed setting to navigate through fishing spots without scaring the fish away.
  • Slow down the trolling motor when making tight turns to avoid prop wash interference and ensure the boat is still moving forward.
  • Use short bursts of power to make minor course adjustments when positioning the boat.
  • Always keep an eye on the battery power levels and switch to the reserve battery if the primary one is running low.
  • Minimize unnecessary movements and vibrations on the boat to avoid spooking the fish.

Tactics for Conserving Battery Life

Running out of battery power can ruin your fishing trip. Here are some tips to conserve the trolling motor’s battery life:

  • Invest in a high-quality deep cycle marine battery and a smart battery charger for efficient recharging.
  • Reduce the trolling motor speed setting when moving against currents or winds.
  • Use the drift function of the trolling motor to move with the breeze or current without consuming battery power.
  • Limit your fishing trips to shorter durations, so you can recharge the trolling motor battery more often.
  • Avoid running additional electrical accessories while the trolling motor is in use to prevent power drain.

Adjustments for Different Water Conditions

The trolling motor’s performance can vary depending on the water conditions. Here are some factors to consider and the adjustments you may need to make:

Water ConditionAdjustment Required
WindIncrease the trolling motor thrust power or use drift mode to move with the wind while conserving battery power.
CurrentUse a higher thrust setting to counter the current speed and maintain boat position or use the locked-in GPS feature if available.
Shallow WaterReduce the trolling motor speed setting to avoid prop wash interference and protect the propeller from damage.
Deep WaterUse a higher thrust setting to move the boat faster and navigate through the water quickly.

Upgrades and Accessories for Enhanced Functionality

There are several upgrades and accessories you can add to your pontoon boat to enhance your trolling motor’s functionality:

  • Wireless Foot Pedal: Offers hands-free operation and eliminates the need for cables and wires on your pontoon floor.
  • GPS Lock: Helps you hold boat position and navigate more easily, especially in challenging water conditions.
  • Prop Guards: Protects your trolling motor propeller from damages that may occur while navigating through shallow waters.
  • Solar Panel: Provides a sustainable way to recharge your trolling motor battery while enjoying your fishing trips.
  • Tilt Brackets: Allows you to adjust the trolling motor’s angle for optimal boat performance and maneuverability.
Key Data PointsDescription
Best Practices for Maneuvering with a Trolling MotorLowest speed setting, slow down during tight turns, short bursts of power, monitor battery power, minimize movements and vibrations on the boat
Tactics for Conserving Battery LifeInvest in high-quality battery and charger, reduce speed setting when moving against wind/current, use drift function, limit fishing trip duration, avoid running additional electrical accessories
Adjustments for Different Water ConditionsIncrease thrust power or use drift mode for wind, use higher thrust setting or GPS lock for current, reduce speed for shallow water, use higher thrust for deep water
Upgrades and Accessories for Enhanced FunctionalityWireless foot pedal, GPS lock, prop guards, solar panel, tilt brackets

Troubleshooting and Maintenance

Routine Maintenance Checks for Longevity

Regular maintenance checks play an important role in extending the lifespan of your through deck pontoon trolling motor. Here are some routine tasks to keep your trolling motor in top shape:

  • Check the propeller for any damage, wear and tear, and debris buildup, and clean it if necessary
  • Inspect the wiring for any signs of fraying or damage
  • Ensure the battery terminals are tight, clean, and free of corrosion
  • Check the thrust bushing for any signs of damage or wear, and replace it if needed
  • Lubricate the moving parts and joints of the trolling motor with a silicone-based lubricant periodically

Identifying Common Issues with Through Deck Trolling Motors

Even with regular maintenance, you might face some issues with your through deck trolling motor. Here are some common problems and their possible causes:

The trolling motor doesn’t turn onDead battery, faulty wiring, blown fuse, defective switch, or damaged motor
The trolling motor turns on but doesn’t run or produce enough thrustWeak battery, damaged propeller, worn-out bushings, or clogged propeller
The trolling motor runs but produces weird noises or vibrationsLoose bolts or screws, damaged propeller, worn-out bearings, or clogged propeller

How to Troubleshoot Trolling Motor Problems

If you encounter any trolling motor problems, here are some troubleshooting steps you can follow:

  1. Check the battery voltage and charge it if needed. A fully charged battery should read around 12.8 volts.
  2. Check the wiring connections for any loose or corroded terminals. Clean and tighten them if necessary.
  3. Check the propeller for any damage, wear and tear, or debris buildup. Clean or replace it if needed.
  4. Check the thrust bushing for any signs of damage or wear. Lubricate or replace it if necessary.
  5. Test the motor by connecting it directly to a battery. If it runs, the motor is fine, and the problem might be with the wiring or control system.
  6. Check the control system for any blown fuses, defective switches, or damaged wiring. Replace or repair them as needed.

When to Call a Professional for Repairs

While some trolling motor problems can be fixed with simple troubleshooting, others might require professional repairs. Here are some signs that you should seek the help of an expert:

  • The trolling motor has suffered physical damage, such as impact, immersion, or exposure to extreme temperatures.
  • The trolling motor has a persistent problem that you can’t diagnose or fix on your own.
  • You don’t have the necessary tools, skills, or knowledge to perform the repairs safely and correctly.


1. How long does a trolling motor battery last on a pontoon boat?

The battery life of a trolling motor on a pontoon boat can vary depending on several factors, such as the battery type, capacity, and usage. However, you can estimate the battery life by dividing the ampere-hour (Ah) rating of the battery by the average amp draw of the motor. For example, if you have a 50 Ah battery and your motor draws 25 amps per hour, your battery would last for about 2 hours at full throttle.

2. Can I use a regular marine battery for my trolling motor?

You can use a regular marine battery for your trolling motor, but it might not provide the best performance and longevity. Trolling motor batteries are designed to withstand the heavy loads, frequent charging and discharging cycles, and harsh marine environments. Therefore, they usually have higher amp-hour ratings, thicker plates, and dual-purpose capabilities for cranking and deep cycling.

3. How do I winterize my through deck trolling motor?

To winterize your through deck trolling motor, follow these steps:

  1. Clean the motor and propeller with fresh water, and let them dry completely.
  2. Grease the fittings and moving parts with a water-resistant lubricant.
  3. Disconnect the battery cables and remove the battery from the boat.
  4. Store the battery in a cool and dry place, and recharge it every two months to maintain its health.
  5. Cover the trolling motor and the boat with a tight-fitting cover to prevent dust, moisture, and pests.

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