Studies of Lake Pontchartrain benthic invertebrates and submersed aquatic vegetation (SAV) from 1996 through 2005 provided the opportunity to determine community responses to severe disturbances including: recovery from shell dredging; effects of anoxia and hypoxia from saltwater intrusion; the 1997 Bonnet Carré Spillway opening; a prolonged drought resulting from an El Niño Southern Oscillation; and effects of Hurricane Katrina. We included reviews and updates of our recently published work, an integrated analysis of findings, and restoration recommendations. During this decadal study there were no prolonged periods of “normal” conditions. Instead, benthos and SAV were experiencing or recovering from significant temporal disturbances. This made it difficult to use the abundance of a particular set of organisms at a point in time to evaluate habitat quality or restoration success without considering past disturbance effects. Benthos species diversity and the relative abundance of stress tolerant groups such as annelids were good indicators of short-term adverse conditions, but rapid changes occurred in response to salinity and dissolved oxygen. Rangia cuneata was a good indicator of the extent of hypoxia and long-term damage from hurricanes. The distribution and abundance of SAV decreased with turbidity and nutrient increases, and Vallisneria americana and other freshwater SAV decreased with prolonged salinity increases. Resistance to and resilience after disturbances and natural changes during long term cycles have to be considered in evaluating habitat condition and restoration success.