Coastal-delta groundwater models must represent aquifer heterogeneity, hydrologic inputs, river–aquifer exchange, and lateral and deep hydraulic connections, but their relative importance can change with the forecast target. We used an observation-informed three-dimensional variable-density groundwater-flow and salinity-transport model of the Pearl River Delta to compare 300 configurations over a five-year simulation. Eight controls were examined: facies structure, spatial variability in hydraulic conductivity (<em>K</em>) within a fixed facies structure, recharge, river stage, riverbed conductance, inland boundaries, coastal boundaries, and model-bottom elevation. Facies structure produced the largest regional head response, and changes in hydrogeologic geometry and connectivity exerted a greater influence than within-facies <em>K</em> variability. Recharge produced widespread responses and the largest changes in volume-weighted mean total dissolved solids (TDS) and in the volumes of brackish-or-more-saline and high-salinity groundwater. Coastal boundaries generated the largest spatial TDS differences, concentrated in estuarine and nearshore aquifers. River-stage effects exceeded riverbed-conductance effects and followed the distributary network, whereas inland-boundary effects were concentrated near hydraulically connected margins. Within-facies <em>K</em> variability produced smaller, spatially dispersed responses, and model-bottom elevation had little influence over five years under the tested bedrock conditions. Model-development priorities depend on the prediction target, area of interest, and spatial and temporal scales. Short-term regional forecasts require reliable initial head and salinity fields, a credible three-dimensional heterogeneous hydrogeologic framework, and well-constrained recharge. Boundary and deep-domain detail become more important near hydraulically connected margins and over longer periods. The perturbation approach and resulting insights are applicable to similar coastal-delta and estuarine aquifers.