Island County is comprised of two islands, the northern end of each separated from the mainland by a rocky channel in the one case and a thin slough in the other. The major portion of the larger of the islands being remoter from the mainland than is that of the smaller, steady development in isolation could explain the greater of these island having become a single county. Meanwhile, easier communication between the mainland and the lesser island invites the question as to why this lesser island does not instead belong to the comparatively large adjoining mainland county of Skagit. Before a bridge connected the big island to the mainland, travel to it from either the small island or from the mainland was by boat or ship, whereas passage between the small island and the mainland was a mere horse-bridge. Even today with bridge and highway the route that takes you from one island to, eventually, the other is rather circuitous, passing through more than a bit of Skagit County along the way. So how came it to be that little Camano Island was never a part of Skagit County, but instead belonged to Island County, the latter of which has always had its seat on the shores of the more distant Whidbey Island?
Some brief Wikipedia-ing indicates to me you need to do some more basic research on the history of these counties. The original county was Island County which then budded off Whatcom (including later Skagit and San Juan counties) and later Snohomish. So the question is rather, why did Island County split into Island and Snohomish along these borders.
Most county definitions came into being when travel by water was easier and more common than travel by land. So, when the county was organized, it is very likely that it included areas that were easy to access from the county seat, by watercraft.
A parallel example occurs in Louisiana, where all the parishes below Baton Rouge lie on both banks of the Mississippi River. Today, that river is a serious impediment to travel, but when the parishes were demarcated, it was easier for the parish authorities to travel across the river, than a few miles overland to interior communities.