Aquaculture plays a strategic role in food security and rural development in coastal regions. However, structural, economic, and institutional constraints affect small-scale producers in heterogeneous ways. This study analyzes how small-scale aquaculture producers in Manabí (Ecuador) perceive the main challenges affecting their activity, based on a typology comprising three production systems: Backyard, Transitional, and Commercial. A structured questionnaire was administered to 98 producers, including 20 variables assessed using a five-point Likert scale. The analysis combined non-parametric univariate tests (Kruskal–Wallis with Dunn post-hoc comparisons) and multivariate techniques to identify statistically significant differences and structured perception patterns across production systems. Significant differences were detected in variables related to biological input supply, market conditions, and structural production constraints. In particular, larvae and fingerling supply, selling prices, buyer availability, and pond surface area showed differentiated perception patterns across systems. Most differences occurred between Backyard farms and the other two production systems, while Transitional and Commercial farms displayed more similar perception profiles. Transversal constraints shared across systems included high feed costs, energy expenditure, and regulatory requirements. Principal Component Analysis identified two main perception gradients related to market and input constraints and to structural and managerial limitations. Discriminant analysis further confirmed the ability of these dimensions to differentiate production systems. These findings highlight the multidimensional nature of constraints affecting small-scale aquaculture and suggest that production systems are better interpreted as gradients of pressures rather than strictly discrete categories. The results underline the need for adaptive governance approaches combining transversal measures with system-specific interventions. Overall, the study provides empirical evidence to support the design of differentiated and context-sensitive policies aimed at strengthening the sustainable development of small-scale aquaculture in Manabí and similar territories.