Science Process Skills (SPS) are essential for developing scientific literacy and critical thinking, yet many students struggle with applying these skills in real-world contexts. This study investigated 12th-grade students’ basic science process skills (SPS) through a contextual-based chemistry practicum, addressing the persistent gap between content mastery and authentic scientific competencies at the end of secondary education. An explanatory sequential mixed-methods design was employed with 36 purposively selected high-achieving students from SMAN 1 Anggana, using validated observation rubrics (37 activities across five indicators), student worksheets, and semi-structured interviews with students and the chemistry teacher to triangulate findings. SPS indicators included observing, measuring (tools and reagents), inferring, classifying, and communicating; scores were converted to percentages and categorized using a five-level scale. The overall mean SPS achievement was 44.97% (“fair”), revealing uneven mastery across indicators despite the sample’s high academic standing. Observing was “excellent” (93.75%) and measuring with reagents was “excellent” (91.67%), whereas measuring with instruments was “very poor” (18.75%) and scientific report writing was “very poor” (0%), indicating limited hands-on experience with instrumentation and insufficient scaffolding for scientific communication. Inferring was “poor” (36.81%) and classifying was “fair” (60.42%), suggesting challenges in integrating empirical data with chemical concepts (e.g., Winkler DO calculations) and applying criterion-based justification for water-quality judgments. Qualitative evidence corroborated that prior “recipe-style” practicums emphasized procedural compliance over evidence-based reasoning, constraining higher-order skills development. The findings support contextual practicum as a diagnostic vehicle to surface differential SPS profiles and inform targeted interventions that shift from procedural verification to problem-based inquiry with authentic, sustained SPS assessment and explicit training in instrumentation and scientific argumentation.