Sand and gravel mining creates novel ecosystems along the Platte, Loup, and Elkhorn rivers in Nebraska, USA. Piping plovers and least terns are state and/or federally threatened and endangered species, respectively, that nest and raise young at these sites and their derivatives. Despite hosting relatively large numbers of piping plovers and least terns for decades, an important question that has largely gone unaddressed is whether the industry that has produced these novel ecosystems is stable and will continue to produce habitat consistently in the future. We evaluated how the number, size, and spatial distribution of different site types hosting different numbers of nesting plovers and terns have changed over time and how current trends in the number of different site types will affect future habitat using a multi‐state modeling approach. Overall area and total number of sites declined during the period 1993–2020. More important, one site type, traditional mines, are being replaced by another site type, modern mines, which host lower numbers of nests of both species. The difference between these two site types is primarily how waste sand is stored. Traditional mines store waste sand in spoil piles or plumes along the edge of a lake created by the mining process, forming relatively large expanses of nesting habitat used by both species. Modern mines store waste sand in limited quantities along the edge of the lake but also in piles away from the lake. Traditional mines also differ from modern mines in that they are routinely converted to housing developments with intermediate transition sites that host the largest number of nests for brief periods. Based on the previous 28 yr of decline, traditional mines and their productive derivatives are projected to continue to decline, thereby further reducing overall nesting habitat. Piping plovers and least terns are expected to nest in our study sites for the foreseeable future, but overall numbers are expected to be smaller than what has been observed in previous decades. Local declines in our study area will have local and regional implications for the recovery and management of these two species of conservation concern.