The present study developed a web-based argumentation program (WAP) to support the science concept and argumentation learning of low achievers (LAs) in socio-scientific issue (SSI) contexts. A quasi-experimental design was applied in the present study. A total of 63 eighth-grade LAs were defined as the experimental group, while 62 of their peers who were medium achievers (MAs) were defined as the control group. The WAP was developed based on three principles to address the specific needs of the LAs: visualizability, interactivity, and multiplicity. The statistical results showed that both the MAs and LAs exhibited significant improvements in both conceptual learning and argumentation learning. However, the LAs acquired better and more balanced improvement in their science argumentation learning. They even outperformed their peers in the MA group in terms of using level 1 claims and qualifiers in the WAP. Meanwhile, the qualitative analysis showed that both the LAs and MAs had no problems with using claims, warrants, or rebuttals. Most of the LAs basically saw the SSI argumentation as a competition and understood that they could potentially strengthen their arguments by citing evidence. However, they found it difficult to construct higher level qualifiers because they had difficulty perceiving the limitations of their own arguments. The co-constructions in the WAP were a main factor influencing the degree and sequence of the LAs' improvements in using claims, warrants, and rebuttals. We subdivided their co-constructions into two types: opposed and supportive. The two types of coconstructions provided the students with various paths through which they can reflect on and evaluate their knowledge. This indicates that there is much potential for the further development of web-based scaffolding in order to facilitate argumentation learning for LAs.