The fish community in the marshes of the Florida Everglades is subject to huge seasonal fluctuations in the amount of flooded marsh, and thus of habitat. During the wet season, as the flooded area increases, the small fish community spreads across the flooded landscape and grows in population size. During the drying phase, the fish are crowded into smaller areas of permanent water. There they are exploited by higher trophic levels, such as wading birds, piscivorous fish, reptiles, and mammals. We develop a landscape simulation model of the lower trophic level food web that includes the small fish community, in which the various trophic levels are described by differential equations. Annual fluctuations in water level are represented by sinusoidally changing hydrology, resulting in dynamic patterns of flooded and non-flooded areas. In this paper we focus on describing the theoretical framework of the model and an analysis on a scenario with annual water level amplitude of 0.6 m. Within these gradients the fish are allowed to disperse and exploit the different habitat resources. To examine how the trophic levels react to annual changes in the water level, long-term simulations over a period of 10 years are performed. The model takes into account the seasonal flooding and drying over an area of many square kilometers, and predicts biomasses of fish across a heterogeneous landscape over time.