Abstract Background In 2010, the Ministry of Health and Sanitation in Sierra Leone launched their Free Health Care Initiative (FHCI) for pregnant and lactating mothers and children under-5. Despite an increase in the update of services, the inequitable distribution of health services and health facilities remain important factors underlying the poor performance of health systems to deliver effective services. This study identifies current gaps in service delivery across two rural locations served by the same District Health Management Team (DHMT). Methods We employed a cross-sectional household survey using a two-stage probability sampling method to obtain a sample of the population across two rural locations in Bonthe District: the riverine and the mainland. Overall, a total of 393 households across 121 villages were surveyed in the riverine and 397 households across 130 villages were sampled on the mainland. Maternal health, child health and sanitation indicators in Bonthe District were compared using Pearson Chi-Squared test with Yates’ Continuity Correction across the two areas. Results Women across the two regions self-reported significantly different uptake of family planning services. Children on the mainland had significantly greater rates of health facility based deliveries; being born in the presence of a skilled birth attendant; completed immunisation schedules; and higher rates of being brought to the health centre within 24 h of developing a fever or a suspected acute respiratory infection. Households on the mainland also reported significantly greater use of treated water and unrestricted access to a latrine. Conclusions If the government of Sierra Leone is going to deliver on their promise to free health care for pregnant women and their children, and do so in a way that reduces inequalities, greater attention must be paid to the existing service delivery gaps within each District. This is particularly relevant to health policy post-Ebola, as it highlights the need for more contextualised service delivery to ensure equitable access for women and children.