The poorly drained pine flatwoods of the Lower Coastal Plain of the Southern United States, including Florida, contain many pond cypress (Taxodium ascendens) wetlands, which cover about one-third of the area. Management of the resource includes pine silviculture and cypress harvesting for lumber, plywood, paper, and mulch. Concern about the ecological impacts and hydrologic effects prompted a cooperative study of cypress wetlands integrating several disciplines. This paper reports results of clear-cut harvesting on the wetland hydrology. Three wetlands of about 0.5 ha were selected and instrumented to measure the climatic and hydrologic variables before and after treatments from January 1993 to January 1997. Silvicultural treatments were wetland-only clear-cut harvesting, wetland plus surrounding upland clear-cut harvesting, and an undisturbed control. The absence of observable soil surface runoff (high infiltration rate) and slow ground-water movement in the upland pine flatwoods suggested that normally the precipitation and evapotranspiration balanced each other and that the wetlands generated most of the runoff from the landscape mosaic as a whole. However, the results showed that open-water evaporation after wetland harvesting exceeded evapotranspiration of the control, explaining in part a decrease in outflow after wetland-only harvesting. Increased runoff from the pine upland, generated by reduced evapotranspiration and expanded saturated areas after clear-cut harvesting, apparently was buffered to some extent by increased evaporation from the embedded clear-cut cypress wetland. The average open-water area was about fifty percent larger than the wetland area as defined by the vegetation. However, excess wetland water balance data suggested the presence of a rain-catchment area that was 2–3 times larger than the vegetative wetland area because of semi-saturated soil in the low slopes. Therefore, the actual catchment area of a cypress wetland in the pine flatwoods may be variable in time, space, and silviculture depending on the topography, the extent of open water, and saturated soil. The application of this information in water management is for better control of first-year runoff from the pine-cypress landscape as a whole. Furthermore, silvicultural Best Management Practices for cypress wetland water management need to consider a variable source area for surface-water pollution that is larger than the wetland area as defined by the vegetation.