Tourism is one of the most important issues facing marine protected areas (MPAs) and small islands worldwide. Tourism development is considered a contribution to pollution levels in the environment. This paper aims to evaluate the hypothetical effects of tourism development on water quality spatially and temporally using the coastal water quality index (CWQI) and Geographic Information System (GIS) in search of improved management for marine conservation areas. This study showed significant tourism influences on the CWQI in the Marine Tourism Park of the Gili Matra Islands, Lombok, Indonesia. Water quality variability indicates a significant spatiotemporal difference (
p
< 0.05) in the two tourism seasons. During the peak season of tourism, the CWQI decreased to poor conditions, i.e., ranging from 9.95 to 21.49 for marine biota and from 7.98 to 30.42 for marine tourism activities in 2013, and ranging from 39.52 to 44.42 for marine biota and from 44.13 to 47.28 for marine tourism activities, which were below the standard for both marine biota and marine tourism activities. On the contrary, it showed a better level (from poor to moderate) during the low season of tourism (ranging from 41.92 to 61.84 for marine biota and from 48.06 to 65.27 for marine tourism activities in 2014), providing a more acceptable condition for both aspects. The study proved that massive tourism development in the MPA and small islands could reduce water quality and increase vulnerability. Accordingly, integrated tourism management and the environment, waters, and land will be needed to develop sustainable tourism. The CWQI and GIS were applicable to assess water quality, both spatially and temporally, and become a quick reference in monitoring and initial evaluation of impact management.