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This paper characterizes non-indigenous fish species (NIS) and analyses both atmospheric and sea surface temperatures for the Mediterranean coast of Egypt from 1991 to 2020, in relation to previous reports in the same areas. Taxonomical characterization depicts 47 NIS from the Suez Canal (Lessepsian/alien) and 5 from the Atlantic provenance. GenBank accession number of the NIS mitochondrial gene, cytochrome oxidase 1, reproductive and commercial biodata, and a schematic Inkscape drawing for the most harmful Lessepsian species were reported. For sea surface temperatures (SST), an increase of 1.2 °C to 1.6 °C was observed using GIS software. The lack of linear correlation between annual air temperature and annual SST at the same detection points (Pearson r) could suggest a difference in submarine currents, whereas the Pettitt homogeneity test highlights a temperature breakpoint in 2005–2006 that may have favoured the settlement of non-indigenous fauna in the coastal sites of Damiette, El Arish, El Hammam, Alexandria, El Alamain, and Mersa Matruh, while there seems to be a breakpoint present in 2001 for El Sallum. This assessment of climate trends is in good agreement with the previous sightings of non-native fish species. New insights into the assessment of Egyptian coastal climate change are discussed. [ABSTRACT FROM AUTHOR]