Ibrahima Bah, who has previously been charged with facilitating illegal entry to the UK, was remanded in custody and ordered to appear at a further hearing on May 15.
The charges relate to the capsize of an inflatable boat packed with migrants which got into trouble in freezing temperatures in December last year.
A rescue operation plucked 39 people from the water and took them to safety. But four others were pronounced dead.
Their identities remain unknown. A coroner's inquest has been told they may have been from Senegal and Afghanistan.
The capsize came just over a year after at least 27 people died in the Channel trying to reach the UK from northern France.
More than 45,000 migrants attempted the perilous crossing last year, a record.
The UK government vowed to tighten the country's borders after it left the European Union.