In Bernoulli's equation, the work done on fluid at the lower end of a pipe is considered negative due to the established sign convention that defines upward movements and forces as positive, while downward movements and forces are negative. This convention is crucial for maintaining consistency throughout the derivation of the equation. Gravitational potential energy (GPE) is treated similarly, increasing as an object moves upward and decreasing as it moves downward, reflecting the negative work done by gravity. The potential energy term in Bernoulli's equation is based on this principle, calculated as density multiplied by gravitational acceleration and height. Adhering to this sign convention ensures that the results of the equation remain valid regardless of the chosen reference point.