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Use mkgmap’s --generate-sea switch. http://www.cferrero.net/maps/mkgmap_tiddlywiki.html#–generate-sea
The simplest would be to create a custom mkgmap style file by renaming the default style and editing the various files to remove OSM objects that you don’t want to appear in your Garmin map. See http://www.cferrero.net/maps/guide_to_mkgmap_style_files.html