The introduction of anthropogenic sound to coastal waters is a negative side effect of population growth. As noise from boats, marine construction, and coastal dredging increases, environmental and behavioral monitoring is needed to directly assess the effect these phenomena have on marine animals. Acoustic recordings, providing information on ambient noise levels and transient noise sources, were made in two manatee habitats: grassbeds and dredged habitats. Recordings were made over two 6-month periods from April to September in 2003 and 2004. Noise levels were calculated in one-third octave bands at nine center frequencies ranging from 250 Hz to 64 kHz. Manatee habitat usage, as a function of noise level, was examined during four time periods: morning, noon, afternoon, and night. Analysis of sightings data in a variety of grassbeds of equal species composition and density indicate that manatees select grassbeds with lower ambient noise for frequencies below 1 kHz. Additionally, grassbed usage was negatively correlated with concentrated boat presence in the morning hours; no correlation was observed during noon and afternoon hours. This suggests that morning boat presence and its associated noise may affect the use of foraging habitat on a daily time scale.