AbstractThe mapping of habitats is the first step that is done in policies that target theenvironment, as well as in spatial planning and management. The biodiversityplans are always centered around habitats. Therefore, constant monitoring ofthese delicate species in terms of health, changes, and extinction is a must inbiodiversity plans. Human activities are constantly growing, resulting in theextinction of land and marine habitats. Land habitats are being destroyed using airpollution and the cutting of forests. At the same time, marine habitats are beingdestroyed due to acidification of ocean waters and waste materials from theindustries and pollution. The author has focused on aquatic habitats in thisdissertation, mainly coral reefs. An estimate of 27% of coral reef ecosystems havebeen destroyed, and a further 30% are at risk of being damaged in the comingyears. Coral reefs occupy 1% of the ocean floor, and yet they provide a home to30% of marine organisms. To analyze the health of these aquatic habitats, theyneed to be assessed through habitat mapping. Habitat mapping shows thegeographic distribution of different habitats within a particular area. Marinehabitats are typically mapped using camera imagery. The quality of underwaterimages suffers from the characteristics of the marine environment. This results inblurry images or containing particles that cover many parts of an image. Toovercome this, underwater image enhancement algorithms are used to preprocessimages beforehand. Now, there are many underwater image enhancementalgorithms that target different characteristics of the marine environment, butthere is no consensus among researchers about a single underwater technique thatcan be used for any marine dataset. In this dissertation, multiple experiments onvarious popular image enhancement techniques (seven) were conducted and usedto reach a decision about a single underwater approach for all datasets. Thedatasets include EILAT, EILAT2, RSMAS, and MLC08. Also, two state-of-the-artdeep convolutional neural networks for habitat mapping, i.e., DenseNet andMobileNet tested. Maximum results from the combination of Contrast LimitedAdaptive Histogram Equalization (CLAHE) achieved as underwater imageenhancement technique and DenseNet as deep convolutional network.