Mothers who use substances often experience gender‐based and structural inequities that can jeopardize maternal and family wellness. Instability in the availability of services, particularly during public health crises (e.g., COVID‐19 pandemic), often results in changes in population health needs/funding/services, which may magnify experiences of disadvantage. Limited research has focused on times of change/crisis and its impact on maternal and family wellness. We examined the experiences of structural disadvantage, service access, and well‐being among mothers who use or formerly used substances during the first year of the COVID‐19 pandemic. Semi‐structured interviews were conducted with 26 mothers with current or past engagement in outpatient substance use treatment programs for pregnant and parenting women in Ontario, Canada. Transcripts were analysed using reflexive thematic analysis, revealing that instability of services and decreased access to/quality of informal and formal relationships often magnified the mental and affective toll of stressors, both pre‐existing and new. The impact on well‐being appeared to be greater for families who were actively engaged with child protective services. Findings are discussed in relation to literature examining systemic and societal factors that perpetuate gender‐based and structural inequities experienced by mothers with lived and living histories of substance use. The potential impact of changes in public health service delivery requires thoughtful and proactive attention for and by all stakeholders, including integrated attention across systems (e.g., health, social, education) that provide services to support maternal and family well‐being.