In science education, only teachers that are competent in skills, methods and procedures relevant to a science discipline can help learners to develop scientific skills and processes associated with investigating natural phenomena. The purpose of this study was to explore views of pre-service science teachers with regard to science process skills that they had developed through various freshwater activities and the stepwise scientific process. Data were collected through a 4-part questionnaire that included various science process skills and the scientific process. Ninety-four 2nd- and 3rd-year pre-service teachers that registered for a Bachelor of Education degree participated in this study. The results from statistical analyses of the teachers' responses to skills they had developed showed prominence of observing, yet the teachers failed to link observing and communication to formulating a research question. Similar challenges were also evident in designing experiments. While the teachers were able to link science process skills to hypothesising, they experienced relative challenges in linking relevant skills to observation and drawing conclusions and making inferences. The findings suggest potential challenges to teachers on fair testing investigations in terms of questioning, designing of experiments, drawing of associated conclusions and making inferences.