Many-flowered navarretia forms mats 2.0 to 7.9 inches across and 0.4 to 1.2 inches high. The stems have a peeling, white surface and are highly branched. Stem thickness is 0.03 to 0.06 inch and is more or less uniform throughout its length. The leaves are 1.2 to 1.6 inches long and are either entire or have a few thread-like lobes. Flower heads are 0.6 to 0.8 inch across and contain between 10 and 60 pale blue flowers. Each flower in the head is 0.20 to 0.24 inches long. Each fruit may contain as many as three seeds. The fruit of this species is a papery capsule that breaks open only when wet.

Little is known about the life history and demography of many-flowered navarretia. Like many vernal pool annuals, its seeds germinate underwater and flower after the pools dry. The plants flower in May and June. The flowers are probably insect-pollinated. Navarretias with similar flowers that occur outside of vernal pools are pollinated by a variety of bees and bee flies, although other insects may visit to collect nectar.

Many-flowered navarretia is found in pools that form on volcanic substrate, specifically in Northern Basalt Flow and Northern Volcanic Ashflow Vernal Pools. Typical many-flowered navarretia is found only at Boggs Lake. The lake itself is classified as a northern volcanic ashflow vernal pool which consists of a clay layer that is impervious to water and is buried under a layer of volcanic ash. The soil at Boggs Lake is in the Collayomi-Aiken-Whispering complex. Elsewhere, Many-flowered navarretia occurs in vernal pools, vernal lakes and swales.