The coastline of the shire is dominated by the Kockatea formation, formed in the Triassic period and consisting of shale, minor siltstone and sandstone. Beekeepers Nature Reserve lies on the Lesueur Sandstone formation, which consists of quartz sandstone with subordinate granule conglomerate and minor siltstone. To the east, the Eneabba formation, formed during the Jurassic period, is interbedded with red-bed sandstone and siltstone. The coastal landscape is dominated by the flat sandy soils of the Swan Coastal Plain. Inland, the terrain is undulating and includes a number of fresh water lakes and streams.
The shire is located within the Dandaragan Plateau (SWA01), Perth Swan Coastal Plain (SWA02) and Northern Jarrah Forest (JAF01) IBRA sub-regions and is characterised by Jarrah and Marri woodlands and Banskia heath on sandy soils. Ten Threatened Ecological Communities (TECs) are found in the shire. These include three national TECs, the vulnerable Subtropical and Temperate Coastal Saltmarsh, the endangered Banksia Woodlands of the Swan Coastal Plain and the critically endangered Claypans of the Swan Coastal Plain. The other TECs are the Shrublands and Woodlands on Perth to Gingin Ironstone, the Shrublands and Woodlands on Muchea Limestone, the Forests associated with deep seasonal wetlands on the Swan Coastal Plain, the Saline Shrublands of Clay Pans, the Dense Shrublands of Clay Flats, Shrublands on Dry Clay Flats and the Melaleuca Shrublands on Limestone Ridges. Gingin Brook and the Moore River are home to important populations of the endangered Western Dwarf Galaxias Galaxiella munda and the vulnerable Carter’s Freshwater Mussel Westralunio carteri, as well a high diversity of other freshwater fish and crayfish species. A large part of Jurien Bay Marine Park is also located off the coast of the shire. The islands in the Marine Park are home to endemic species like the vulnerable Lancelin Island Skink Ctenotus lancelini, important haul out and pupping grounds for vulnerable Australian Sea Lion Neophoca cinerea and important breeding grounds for seabirds including Wedge-tailed Shearwater Ardenna pacificus and Roseate Tern Sterna dougalli.
The main land uses in the Shire of Gingin are agriculture, horticulture, residential, recreation and nature conservation. Of the total land area, 37% is arable. The 217, 603 ha total area of agricultural holdings is operated by 94 agricultural businesses and produced agricultural commodities worth $14, 255, 301 gross value in 2016 (ABS 2018).