Following cuts to legal aid the number of people representing themselves in Wales nearly doubled in a year from 2,574 in 2012/13 to 4,920 in 2013/14.
Crispin Masterman said cases took longer to settle without solicitors.
The Ministry of Justice said it recommended mediation as "quicker, cheaper and less stressful" than court.
Family courts are private hearings dealing with financial issues, residence, and access for separated parents to their children, in front of a judge or magistrates.
The Legal Aid, Sentencing and Punishment of Offenders Act 2012effectively removed legal aid for the majority of private family law cases when it came into effect in April 2013.
Judges, magistrates and lawyers have all criticised the new legislation, which they claim prevents vulnerable people from accessing justice, and slows up the family court system to the detriment of the children involved.
Only people who are proven victims of domestic violence, or those challenging care orders being imposed by local authorities through public law proceedings, remain eligible for legal aid.
More than half of all parties in the family courts were unrepresented by a solicitor, according to figures from the Ministry of Justice.
Mr Masterman, who was a designated family judge for Cardiff and Pontypridd, told BBC Wales that the emotional, mental and psychological wellbeing of children involved in such cases risked being damaged by the court process.
He said: "The Children Act says that the welfare of the child is paramount in these cases, which is a given. But it also says delay is the enemy of a child's best interests, and so anything which means that the resolution of a child's interests takes longer, must be damaging to the child."
One mother who is representing herself in court against her ex-husband about access to their children said she has panic attacks because of the process.
"Usually about a week before we go to court, you feel sick, can't sleep, I have panic attacks, I have to take time off work because I don't want to go to work, I'm an emotional wreck. I'm low, I don't eat…I just feel awful.
"You walk in there, I've got no confidence at all…I don't know what to say, what the court procedure is, you just have to follow what they're doing and hope that one day I'll get listened to.
"I don't know much about the legal side of things, all the words or the swagger that they use, so it's very difficult to stand there knowing that he's got legal representation that's going to fight his corner and I'm just stood there on my own."
Mr Masterman said that taking lawyers "out of the equation" in most cases had meant more contested court hearings and longer delays in resolving cases.
He said: "The damage that's done is both emotional and probably, in some cases, psychological as well, and the difficulty is that parents don't see this, they're so tied up in their own issues that they forget that the child's welfare is the paramount issue."
Family law specialist Sophie Hughes warned that some children at the centre of complex cases could even end up in care.
She said: "One can only begin to think about the effect that it has on a child having parents who are spending months, years in some cases, litigating through the court about what the arrangement should be."
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