Ground-water contamination by nonpoint source pollutants is recognized as a major environmental threat to human and the sustainability of healthy ecosystems. In this paper, the authors advective-reactive models that describe transport and fate of pollutants in inclined unconfined aquifers subject to a variable source. The models have implication on nitrate transport and denitrification at depth in aquifers, and the impact this has on attenuating nitrate discharge to streams in agricultural watersheds. The objectives of the models are: (1) to predict the impact of geochemical and physical controls on baseflow loadings in agricultural watersheds; and (2) to develop an index that measures the capacity for nitrate removal in ground water in agricultural watersheds. First, the steady-state ground-water flow problem is solved in two-layered unconfined aquifers with impervious inclined beds. Approximate closed-form expressions are also developed for ground-water fluxes in a two-layer inclined unconfined aquifer. Second, the transport and fate problem is formulated for the two-geochemically distinct layers, and solved in a Lagrangian framework using a regular perturbation technique.