Photovoltaic solar water pumping systems (PVSWPS) offer a sustainable solution for water access in remote rural areas, but their performance strongly depends on accurately tracking the maximum power point (MPP) of the photovoltaic (PV) array, a task complicated by partial shading, which introduces multiple local maxima in the power–voltage characteristic. This study presents the design and simulation of a complete PVSWPS — comprising a PV array, a Ćuk DC–DC converter, a permanent magnet DC motor–centrifugal pump assembly, and a hydraulic network — modeled in MATLAB/Simulink and evaluated under partial shading scenarios representative of the Ecuadorian coast. Three MPPT strategies were implemented and compared: a conventional Incremental Conductance (IC-MPPT) algorithm, a Particle Swarm Optimization-based algorithm (PSO-MPPT) exploiting empirically identified voltage clusters, and an Artificial Neural Network-based algorithm (ANN-MPPT) trained on the irradiance-to-MPP voltage relationship. Results show that IC-MPPT converges to a local maximum in three of five evaluated scenarios, with a mean tracking error of 20.45%, whereas PSO-MPPT and ANN-MPPT maintain mean errors of 0.90% and 1.71%, respectively, increasing cumulative pumped water volume by approximately 5.7% and 5.1%. This gain came with a modest reduction in converter conversion efficiency, revealing a trade-off between tracking accuracy and efficiency that has received limited attention in the literature. These findings support the adoption of intelligent MPPT strategies for photovoltaic water pumping under frequent partial shading conditions.