The coastline of the shire is dominated by the Lancelin formation, formed from the volcanic and sedimentary rock that overlies the Perth Basin and consisting of glauconite chalk, marl and calcareous mudstone. Inland areas are dominate by the Osbourne formation, formed from volcanic and sedimentary rock and interbedded with sandstone, siltstone, shale and claystone. To the east, the Leederville formation is interbedded with sandstone, siltstone and minor conglomerate over thin beds of coal seams and the Coolyena group consists of chalk interspersed with greensand, glauconitic, siltstone, sandstone and marl.
Soils along the coast are sandy, forming part of a complex dune system, and include some gravelly soils over limestone outcrops. The landscape inland is characterised by rolling hills interspersed with rocky outcrops and low-lying floodplains. Soils are deep, pale, siliceous sands and gravels.
The shire is located within the Dandaragan Plateau (SWA01) and Perth Swan Coastal Plain (SWA02) IBRA sub-regions and is characterised by Jarrah and Marri woodlands and Banskia heath on sandy soils. Four Threatened Ecological Communities (TECs) are found in the shire. These are two national TECs, the vulnerable Subtropical and Temperate Coastal Saltmarsh and endangered Banksia Woodlands of the Swan Coastal Plain, as well as the Stromatolite Community of Lake Thetis and the Lesueur-Coomallo Floristic Community D1. The Lesueur-Coomallo region is extremely floristically diverse, supporting ~1,000 plant species, and an important breeding ground for endangered Carnaby’s Black-Cockatoo Calyptorhuncus latirostris. 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 Jurien Bay Skink Liopholis pulchra longicauda, important haul out and pupping grounds for vulnerable Australian Sea Lion Neophoca cinerea, support a population of endangered Dibbler Parantechinus apicalis on Boullanger and Whitlock Islands and provide important breeding habitat for seabirds including Wedge-tailed Shearwater Ardenna pacificus and Roseate Tern Sterna dougalli.
The main land uses in the Shire of Dandaragan are agriculture, residential, recreation and nature conservation. Of the total land area, 51% is arable. The 455, 204 ha total area of agricultural holdings is operated by 196 agricultural businesses and produced agricultural commodities worth $29, 757, 989 gross value in 2016 (ABS 2018).