This study experimentally evaluated the fuel consumption and operating costs of a locally manufactured diesel-powered floating pumping station designed for operation under low river water levels in Iraq. The system consists of four pontoons supporting a centrifugal pump (Rovatti 5″ × 6″) driven by a 51 kW DEUTZ diesel engine. A factorial experiment was conducted in 2024 using three water depths (2, 2.5, and 3 m), three pump speeds (1500, 1600, and 1700 rpm), and three discharge pressures (2.5, 3.0, and 3.5 bar) with three replications in a completely randomized design. Fuel consumption was measured in L·h⁻¹ and economic analysis was performed to estimate fixed, variable, and total operating costs (ID·h⁻¹). The results showed that pump speed significantly affected fuel consumption and total operating costs (p ≤ 0.05). Increasing speed from 1500 to 1700 rpm increased fuel consumption from 5.14 to 11.49 L·h⁻¹, leading to a substantial rise in hourly operating costs. Discharge pressure also influenced fuel consumption, whereas water depth had no significant effect within the tested range. The lowest total operating cost was achieved at 1500 rpm under 3.5 bar discharge pressure. Economic analysis indicated that fuel costs constituted the largest proportion of total variable costs. The findings demonstrate that operating the floating pumping station at moderate engine speeds enhances fuel efficiency and reduces operational expenses. The study provides practical guidelines for optimizing the economic performance of floating pumping systems under fluctuating river water levels.