Ethanol, water and phase separation
Ethanol is hygroscopic: it pulls water straight out of humid air. A vented fuel tank breathes in and out with every temperature swing, and a tank sitting half empty through a New Hampshire winter has a large volume of damp air above the fuel doing exactly that, day after day. The ethanol in the petrol holds that absorbed water in suspension up to a point. Past that point it cannot, and the fuel separates. That is the boat that ran fine in October and will not run in May.
Phase separation leaves two layers in the tank. A heavy water-and-ethanol layer sits on the bottom, which is precisely where the pickup is, and the petrol above it has lost the ethanol that was carrying a good part of its octane. Neither layer will run an engine properly. It does not remix by shaking the boat or by adding fresh fuel on top, and no additive reverses it. The fix is to remove the contaminated fuel, clean the tank out, and refill it.
Water-separating filters are not engine filters
A water-separating filter is not the same thing as the engine's own fuel filter, and a boat needs both. The separator is the larger spin-on canister mounted between the tank and the engine. It works by slowing the fuel down so that water, being denser, drops out into a clear bowl at the bottom where it can be seen and drained off. The small filter on the engine is there to catch fine particles before the injectors or the carburettor, not to hold water.
The bowl should be looked at, not merely replaced on schedule. Water sitting in it means water in the tank, and swapping the element without asking where that water came from means doing the same job again shortly. Rust-coloured sediment points at a steel tank corroding internally. Black, sticky residue is usually degraded fuel and varnish lifted off the tank walls. The separator is the best window into the condition of a tank that does not involve opening the tank.
Tanks, vents and lines
The classic fuel fault runs perfectly for ten minutes, then loses power and dies, restarts after sitting a while, and does the same thing again. That is a vent problem. As fuel leaves the tank, air has to come in to replace it, and if the vent is blocked by a wasp nest, a spider, corrosion or a kinked hose, the tank pulls into vacuum and the pump can no longer draw fuel. Loosening the fill cap and hearing a hiss confirms it on the spot.
Tanks themselves fail in ways worth knowing about. Aluminium tanks corrode from the outside in, where they sit on damp foam or in a wet bilge. Steel tanks rust from the inside. Pickup tubes crack and suck air, which behaves exactly like a starving pump. Fuel lines go hard and permeable with age, and old hose that predates the ethanol-resistant standards breaks down internally and sheds its liner into the filter. ABYC publishes the standards those hoses and installations are built to.
Carburettors and injection after a layup
Carburettors suffer most from storage. The fuel left in the float bowl evaporates and leaves varnish and a green-white deposit behind, and the jets and passages it blocks are measured in thousandths of an inch. The symptoms are a lean stumble, a hesitation off idle, a hunting idle, or no start at all. Cleaning means the carburettor comes off and is dismantled, not sprayed through from outside, because aerosol cleaner does not shift hardened varnish out of a pilot circuit.
Injected engines fail differently. Injectors clog partially rather than completely, so the engine runs rough or down on power under load. High-pressure pumps in the fuel module fail, and water sitting in the system corrodes rails and injector tips. A vapour separator tank that has had fuel decompose inside it needs cleaning out. Priming bulbs and lines matter on both types: a bulb that has gone hard, cracked, or will not hold pressure is a very common no-start.
Storing fuel properly over the winter
Stabiliser works, but only if it actually reaches the fuel it is meant to protect. Pouring it into the tank and then shutting the boat down for the winter leaves the carburettor bowls, the lines, the filter and the injection system full of untreated fuel. The engine has to run long enough afterwards for stabilised fuel to be drawn all the way through the system. That is the step most owners skip, and it is the step that decides whether spring is easy or expensive.
A full tank has less air space above it and therefore less humid air to give up water, which is the main argument for storing full. Where a boat is laid up dry, draining the carburettor bowls and the separator bowl is better still. Either way, fit a fresh water-separating element before the boat goes away for the winter and check that the vent line is clear, so the spring job is a start-up rather than a tank clean-out.