Generally projects and programs need to publicly file Environmental Impact Statements or Environmental Assessments, since the environmental impact of the activities at a place like Kennedy Space Center change over time.
One example is the EIS written for Constellation, which planned to drop some pretty big stuff into the drink. One paragraph from that document states:
NASA has consulted with the National Marine Fisheries Service (NMFS)
on essential fish habitat regarding launches of Ares vehicles from KSC
(KSC 2007e). NASA has indicated to NMFS that over more than 25 years
of Space Shuttle operations, there have been no documented long-term
impacts to marine life or marine habitats. Similarly, the proposed
Constellation Program launches are not expected to produce any
measurable impacts to marine species or habitats.