The biogeochemical cycling of nutrients and oxygen in the coastal ocean is of high importance given that anthropogenic nutrient inputs have doubled the preindustrial nutrient load to water bodies. In particular, excess nitrogen (N) causes eutrophication and hypoxia in the coastal ocean, which is further exacerbated by increased stratification due to global warming. Owing to relatively shallow waters in coastal regions, processes within the sediment and water column play equally important roles in key biogeochemical cycles. To understand the factors that regulate the nutrient and oxygen cycle in seasonally hypoxic coastal basins, this thesis employs high-resolution field observations conducted in Bedford Basin, coupled with numerical modeling, to investigate the impact of various geochemical, biological, and physical drivers. In Chapter 2, field observations of weekly CTD casts and measured benthic oxygen uptake were used to develop and parameterize a numerical model to understand the development of hypoxia in Bedford Basin and quantify different sources and sinks of oxygen in three contrasting years. Chapter 3 is focused on understanding the annual development of the nitrogen cycle based on weekly timeseries of geochemical parameters and phylogenetic marker genes in bottom waters over four consecutive years. Measured geochemical and biological parameters were incorporated into a box model to simulate the nitrification dynamics and identify the controlling factors. Through this approach, a novel mechanism of nitrification was identified whereby strong physical mixing dilutes the resident nitrifier biomass leading to delayed and decoupled nitrification. Weak physical mixing during winter may have the reverse effect. In Chapter 4, benthic biogeochemical processes were studied through seasonal measurements of organic matter remineralization rate, benthic fluxes, sediment geochemical profiles, along with reaction-transport modeling. Overall, this thesis studied the development of hypoxia in a coastal basin, nutrient cycles in the water column and sediment, and the physical and biological drivers of coupled biogeochemical cycles.