The thesis is focused on the ecohydrological prediction and analyses of dissolved oxygen (DO) and biological responses as influenced by the environmental drivers for unit river ecosystems. DO is a prominent indicator for the general health of an aquatic ecosystem. Traditional assessment of surface water quality based on gap samples of discrete DO is often limited by large diurnal fluctuations. A common reference time for DO measurements is needed for a better assessment of the differences among water bodies and for identifying changes with time. Two different models are developed to convert a DO measurement at any diurnal time to that at a reference time. Both models are based on an extended stochastic harmonic analysis (ESHA) developed in this thesis and were evaluated for different stream sites across Minnesota. Data were normalized to increase the general applicability of the fitted parameters. Each of the algorithms revealed good performance in representing observed diurnal variations in DO. The proposed DO models provide useful tools for total maximum daily load (TMDL) assessment of aquatic ecosystem health across a range of spatial and temporal scales. Mechanistic one-zone and two-zone food web models are also developed as part of the thesis. The one-zone model assumes the benthic and nonbenthic (or water-column) zones as one well-mixed tank while the two-zone model considers them as two separate, but interacting biotic habitats. The flow processes, solar radiation, and temperature were considered as the associated dynamic environmental drivers. The objective model state variables were represented by the hierarchical levels of detritus, limiting nutrient, vegetation, and invertebrates. The fish trophic level was included as an input model parameter. Model parameters, constants and boundary conditions were defined based on watershed as well as channel hydrology, stream geomorphology and biological activities by utilizing advances in ecological engineering. The two-zone model was evaluated with nominal or no calibration for a gravel bed prealpine Swiss stream. The model was able to produce the general trends of the food web state variables. Numerical simulation of the river food web and subsequent evaluations are useful in unraveling the underlying mechanisms in aquatic population dynamics.