Eph 4:5 speaks of 'one Lord, one faith, one baptism' yet the New Testament speaks both of baptism in water and of baptism in the Holy Spirit.

We have already seen that in New Testament practice generally conversion, baptism in water, and baptism in the Holy Spirit are so closely connected that they are not clearly distinguished ie there is one baptism which occurs at conversion, shown outwardly by baptism in water and inwardly by the work of the Holy Spirit. This is the baptism into Jesus Christ (Rom 6:3).

Note that John's baptism would be another baptism, and so would baptisms carried out as part of Jewish ritual - but Paul is talking in the context of unity in the Church, so these are irrelevant.