Three 12V lithium batteries or one 36V for a 36V trolling motor?

Direct answer: A single 36V LiFePO4 battery is usually the cleaner choice: one BMS, one charger profile, no series imbalance between separate 12V packs, and fewer cables. Three 12V batteries in series can work only if the maker allows series use, the packs are matched, and you charge them correctly—often with a 36V charger across the string or carefully managed per-battery charging. Flexibility of later reusing 12V units is the main reason to stay with three; reliability and simplicity favour one 36V pack.

One 36V pack. Products such as the 36V 100Ah (about 3.84 kWh) and 36V 50Ah (about 1.92 kWh) are built as a single series string inside one case with one BMS. Size Ah from motor amp draw and hours on the water; see runtime from amp draw (same method at 36V).

Three 12V in series. Three 12V 100Ah packs give a 36V nominal string at 100Ah only if series connection is explicitly allowed on those packs. Many drop-in 12V LiFePO4 batteries limit or forbid series use because the BMS cannot balance across separate packs. Confirm series count, identical age/firmware, and equal cable lengths.

Charging. A 36V lithium charger into a single 36V pack is straightforward. With three 12V packs, a single 36V charger across the string needs packs that tolerate that arrangement; charging each 12V separately is safer for balance but inconvenient on a boat. Do not use a lead-acid wet charger profile.

Failure modes. In a series string, if one 12V BMS opens, the whole motor loses power. A single 36V pack has one protection domain—still a single point of failure, but without inter-pack imbalance. Carry a spare strategy that matches your choice.

Weight and space. One 36V case often uses tray space better than three Group-size 12V batteries plus series jumpers. The 36V 50Ah page lists about 14 kg; three 12V 100Ah packs weigh more and need more interconnects.

When three 12V still wins. You already own matched series-capable 12V packs, or you need to redeploy batteries to 12V house loads in the off season. Otherwise prefer one 36V. Golf-cart 36V packs are a different product family; see 36V golf cart sizes if the tray is a cart tray rather than a boat well.

Commissioning. After wiring, check total voltage, each pack voltage if series 12V, polarity at the motor, fuse size, and a short dock test before open water.